Karachi has become too large for its own health. I think there is a Hadith that when your cities become large, you should move out and found new cities.
The Pathan-Muhajir violence was little to start with. Transport has traditionally been in the hands of the Pathans. I remember in my childhood a gruesome murder when on a small altercation about fare or something, a man was run down in the bus terminus grounds at Karachi. A lot of buses chased him around the grounds of the terminus, and he was simply crushed by them at the end. That caused a lot of bad blood between the two communities, but the real break came in the wake of Ayub Khan's victory over Ms Fatima Jinnah. It was not a direct election, but Karachi, Dacca and perhaps Lahore had voted in favor of Ms Jinnah. The night of election results was a terrible night for Karachiites. The Pathan gangs ran amok, killing and burning and shouting: "You voted against our king, now see the result". That caused a divide which has not been breached yet.
When Altaf Hussain founded his Muhajir Students Organization, and then Muhajir Qaumi Movement, the Muhajor gangs battled similar and older Punjabi and Pathan gangs. His movement was financed by Zia's internal security agencies, to break the power of Jamaate Islami. When MQM managed to wrest almost total control of Karachi, and reached the National Assmebly, Altfa renamed his movement the Muttahida Qaumi Movement. At one time RAW also financed him and trained his cadres.
Kidnappings, extortion, blackmail and torture remained the hallmarks of his movement.
The Pathan is moved by appeal to Pakhtunwali, but there are ideological divide.s, too. Secular (ANP, PPP), Islamists (Jamate Islami, JUI). The present turmoil in Karachi may also be linked to the army operations in the Pathan hinterland. At one time Afghanistan (under the Soviets) unleashed gangs of terrorists in Pakistan.
PPP had started as a secular, modernizing, small man's rights party. It turned back into a feudal entity within Z A Bhutto's tenure as Prime Minister. It is dominated by feudals, and they believe in taking from the state and from the common man. Not in giving anything. Many dacoits are in their pay.
During Zia's time, the PPP was persecuted, and it too received financing and training from India's RAW, Afghanistan's (under the Soviets) KHAD, Syria's Mukhbarat and also Libya. However, Benazir made it an establishment party. She had noted that the road to Pakistan's Prime Ministership is governed by Washington, which is not interested in a social revolution.
Zardari was, and continues to be, a percentage man.
The greatest crimes Musharraf has committed against Muslims and Pakistan was to hand over Muslims to the US for torture, and to issue the NRO which whitened all loot during Benazir's rule. This has allowed Zardari and people like Salman Farooqui to return and control the state machinery.